[CHNOSZ-commits] r567 - in pkg/CHNOSZ: . R inst vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Sun Jul 19 13:09:55 CEST 2020 

Author: jedick
Date: 2020-07-19 13:09:54 +0200 (Sun, 19 Jul 2020)
New Revision: 567

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/equilibrate.R
   pkg/CHNOSZ/R/util.expression.R
   pkg/CHNOSZ/R/util.plot.R
   pkg/CHNOSZ/inst/NEWS.Rd
   pkg/CHNOSZ/vignettes/multi-metal.Rmd
Log:
Improve label formatting and placement of tick marks


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2020-07-18 03:41:12 UTC (rev 566)
+++ pkg/CHNOSZ/DESCRIPTION	2020-07-19 11:09:54 UTC (rev 567)
@@ -1,6 +1,6 @@
-Date: 2020-07-18
+Date: 2020-07-19
 Package: CHNOSZ
-Version: 1.3.6-40
+Version: 1.3.6-41
 Title: Thermodynamic Calculations and Diagrams for Geochemistry
 Authors at R: c(
     person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),

Modified: pkg/CHNOSZ/R/equilibrate.R
===================================================================
--- pkg/CHNOSZ/R/equilibrate.R	2020-07-18 03:41:12 UTC (rev 566)
+++ pkg/CHNOSZ/R/equilibrate.R	2020-07-19 11:09:54 UTC (rev 567)
@@ -376,7 +376,7 @@
   if(is.numeric(balance[1])) {
     # a numeric vector
     n.balance <- rep(balance, length.out=length(aout$values))
-    message(paste0("balance: from supplied numeric argument (", balance, ")"))
+    message(paste0("balance: from supplied numeric argument (", paste(balance, collapse = ","), ")"))
   } else {
     # "length" for balancing on protein length
     if(identical(balance, "length")) {

Modified: pkg/CHNOSZ/R/util.expression.R
===================================================================
--- pkg/CHNOSZ/R/util.expression.R	2020-07-18 03:41:12 UTC (rev 566)
+++ pkg/CHNOSZ/R/util.expression.R	2020-07-19 11:09:54 UTC (rev 567)
@@ -29,9 +29,11 @@
         # append the elemental symbol
         expr <- substitute(paste(a, b), list(a=expr, b=names(elements)[i]))
         # recover the coefficient
-        if(elements[i]==1) coeff <- "" else coeff <- elements[i]
-        # append the coefficient
-        expr <- substitute(a[b], list(a=expr, b=coeff))
+        coeff <- elements[i]
+        if(coeff!=1) {
+          # append the coefficient
+          expr <- substitute(a[b], list(a=expr, b=as.character(coeff)))
+        }
       } else {
         # for charged species, don't show "Z" but do show e.g. "+2"
         coeff <- elements[i]
@@ -38,6 +40,7 @@
         if(coeff==-1) coeff <- "-"
         else if(coeff==1) coeff <- "+"
         else if(coeff > 0) coeff <- paste("+", as.character(coeff), sep="")
+        else coeff <- as.character(coeff)
         # append the coefficient as a superscript
         expr <- substitute(a^b, list(a=expr, b=coeff))
       }

Modified: pkg/CHNOSZ/R/util.plot.R
===================================================================
--- pkg/CHNOSZ/R/util.plot.R	2020-07-18 03:41:12 UTC (rev 566)
+++ pkg/CHNOSZ/R/util.plot.R	2020-07-19 11:09:54 UTC (rev 567)
@@ -216,8 +216,13 @@
   if(!is.null(lwd)) {
     for(thisside in side) {
 
-      ## get the positions of major tick marks and make grid lines
+      ## get the positions of major tick marks
       at <- axis(thisside,labels=FALSE,tick=FALSE) 
+      # get nicer divisions for axes that span exactly 15 units 20200719
+      if(thisside %in% c(1,3)) lim <- par("usr")[1:2]
+      if(thisside %in% c(2,4)) lim <- par("usr")[3:4]
+      if(diff(lim)==15) at <- seq(lim[1], lim[2], length.out = 6)
+      # make grid lines
       if(grid %in% c("major", "both") & thisside==1) abline(v = at, col=col.grid)
       if(grid %in% c("major", "both") & thisside==2) abline(h = at, col=col.grid)
       ## plot major tick marks and numeric labels
@@ -238,7 +243,8 @@
       da <- abs(diff(at[1:2]))
       # distance between minor tick marks
       di <- da / 4
-      if(da %% 2 | !(da %% 10)) di <- da / 5
+      if(!da %% 3) di <- da / 3
+      else if(da %% 2 | !(da %% 10)) di <- da / 5
       # number of minor tick marks
       if(thisside %in% c(1,3)) {
         ii <- c(1,2) 

Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd	2020-07-18 03:41:12 UTC (rev 566)
+++ pkg/CHNOSZ/inst/NEWS.Rd	2020-07-19 11:09:54 UTC (rev 567)
@@ -6,7 +6,7 @@
 \newcommand{\H2O}{\ifelse{latex}{\eqn{\mathrm{H_{2}O}}}{\ifelse{html}{\out{H<sub>2</sub>O}}{H2O}}}
 \newcommand{\Hplus}{\ifelse{latex}{\eqn{\mathrm{H^{+}}}}{\ifelse{html}{\out{H<sup>+</sup>}}{H+}}}
 
-\section{Changes in CHNOSZ version 1.3.6-40 (2020-07-18)}{
+\section{Changes in CHNOSZ version 1.3.6-41 (2020-07-19)}{
 
   \subsection{MAJOR CHANGES}{
     \itemize{
@@ -199,7 +199,7 @@
 
       \item TODO: remove stopifnot() from examples.
 
-      \item TODO: get axis labels at intervals of 5 (0, 5, 10, 15) in thermo.plot.new(c(0, 15), c(0, 15), "x", "y").
+      \item TODO: change default to diagram(., water.lines= FALSE)
 
     }
   }

Modified: pkg/CHNOSZ/vignettes/multi-metal.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/multi-metal.Rmd	2020-07-18 03:41:12 UTC (rev 566)
+++ pkg/CHNOSZ/vignettes/multi-metal.Rmd	2020-07-19 11:09:54 UTC (rev 567)
@@ -79,7 +79,7 @@
 ## Simple Overlay
 
 Simple overlay refers to independent calculations for two different systems that are displayed on the same diagram.
-Although is easy to make such a diagram, there is no interaction between the systems.
+Although it is easy to make such a diagram, there is no interaction between the systems.
 
 This example starts with a log*f*~O<sub>2</sub>~--pH base diagram for the C-O-H system then overlays a diagram for S-O-H.
 The second call to `affinity()` uses the argument recall feature, where the arguments are taken from the previous command.
@@ -246,7 +246,7 @@
 species(c("covellite", "chalcocite", "tenorite", "cuprite"))
 aCu <- affinity(aFe)  # argument recall
 dCu <- diagram(aCu, xlab = xlab)
-title(paste("Only Cu; 1° balance", dCu$balance))
+title(paste("Only Cu; 1° balance:", dCu$balance))
 label.plot("B")
 
 # Only Fe- AND Cu-bearing minerals
@@ -269,7 +269,7 @@
 ad2 <- duplex(d1, dFeCu, balance = "H+")
 abbrv <- info(ad2$species$ispecies)$abbrv
 diagram(ad2, xlab = xlab, balance = 1, names = abbrv)
-title("All Fe or Cu; 2° balance: H+")
+title("Fe and/or Cu; 2° balance: H+")
 label.plot("E")
 
 db <- describe.basis(ibasis = 3)
@@ -364,6 +364,7 @@
 tN <- paste("log(total N in basis species) =", loga_N)
 tC <- paste("log(total C in formed species) =", loga_C)
 title(main = paste(tN, tC, sep = "\n"), font.main = 1)
+legend("topright", legend = lTP(25, 1), bty = "n")
 ```
 
 The diagram shows the expected ionization of acetic acid and NH~3~ at different pHs.

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